Dorfdad,
I've used the first-generation ATVs for years, but like you, I've been unable to stream mkvs. Before buying the new ATV, I've asked around (actually, on these boards) and it seems there's a way to "convert" the mkvs to m4vs easily and then stream them on the new ATV.
There is a free program called Subler. Once downloaded, you can drag the mkv into and it will convert it to an H264 format as an m4v. From there, you can MetaX and drag it into iTunes as usual and then stream it from the new ATV.
Unfortunately, I've only been able to do this in theory, as I've yet to obtain the new ATV and as I've said, this wil NOT work in the first generation ones.
Why not make a COPY of one of your mkvs this way, drag it into iTunes and see if the new ATV will in fact, stream the new file? I suspect many of us are dying to see if this will work. If so, then there is no need to jailbreak anything.
C-Pup